Summary and Schedule
This lesson is where a file should live on the cluster. Home is small and backed up. Scratch is large and temporary. A job has its own directory, and that directory does not last.
The last episode submits work with sbatch. The EESSI
client container has no sbatch, so that episode needs
Snellius or the course cluster.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Why I/O matters |
What is the difference between a metadata server and a data
server? Why do a thousand small files cost more than one file of the same total size? Which of three files belongs on home? ::: |
| Duration: 00h 15m | 2. The file systems |
How long does a file last on home, on scratch-shared, in
$TMPDIR, and on the project space?What does a Snellius quota line say, and what do you run when myquota is not
there?::: |
| Duration: 00h 45m | 3. Files and directories |
How do you see the directory you are in, and how do you make a directory
on scratch? After mv, what does ls
show?What does rmdir print when the directory is not
empty?::: |
| Duration: 01h 20m | 4. Permissions and quota |
What does chmod g-r change in the mode string?How do you see whether home is close to full? ::: |
| Duration: 01h 50m | 5. Space for a job |
What does a job’s $TMPDIR look like, and why do two jobs on
one node get two directories?How do you ask Snellius for scratch-node, and what do you do on a cluster that has no such disk? How do you shrink ex1/run.sh without editing
it?::: |
| Duration: 02h 30m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
You need a terminal and a login. The EESSI client container is the
wrong place for this lesson. It has no sbatch, and the last
episode submits a job.
Snellius
Snellius is the Dutch national supercomputer. SURF sends the account mail. The public description is at https://www.surf.nl/en/services/compute/snellius-the-national-supercomputer.
Sign in to the SURF user portal before the first SSH login. If the network you are on is not trusted, the welcome mail names a door node. Use that host.
Your prompt starts in home. pwd prints
/home/YOUR_LOGIN.
The course cluster
Your trainer sends a setup link and a welcome note. The note has the address and the login. There is one login node.
MANAGER is the address in the welcome note. It is not
snellius.surf.nl. Paths on this cluster are not the
Snellius paths. Each episode’s tab names the ones you have. Do not
create /scratch-shared here. It is not on this machine.
Files from this lesson
episodes/files/ex1/print-n.c and
episodes/files/ex1/run.sh are the last episode’s program.
Submit from that directory, or copy both files into the directory you
submit from. The script loads module load 2025 and
GCC/14.2.0.